PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The effect of repeated laser stimuli to ink-marked skin on skin temperature—recommendations for a safe experimental protocol in humans
items: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system
items: Faces in commonly experienced configurations enter awareness faster due to their curvature relative to fixation
items: A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors
items: Residual mitochondrial transmembrane potential decreases unsaturated fatty acid level in sake yeast during alcoholic fermentation
items: The impact of land reform on the status of large carnivores in Zimbabwe
items: Probable impact of age and hypoxia on proliferation and microRNA expression profile of bone marrow-derived human mesenchymal stem cells
items: Preoperative CT versus diffusion weighted magnetic resonance imaging of the liver in patients with rectal cancer; a prospective randomized trial
items: Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus
items: Acute hypothalamic suppression significantly affects trabecular bone but not cortical bone following recovery and ovariectomy surgery in a rat model

The effect of repeated laser stimuli to ink-marked skin on skin temperature—recommendations for a safe experimental protocol in humans
type: item
type: AcademicArticle
description: Background. Nd:YAP laser is widely used to investigate the nociceptive and pain systems, generating perpetual and laser-evoked neurophysiological responses. A major procedural concern for the use of Nd:YAP laser stimuli in experimental research is the risk of skin damage. The absorption of Nd:YAP laser stimuli is greater in darker skin, or in pale skin that has been darkened with ink, prompting some ethics boards to refuse approval to experimenters wishing to track stimulus location by marking the skin with ink. Some research questions, however, require laser stimuli to be delivered at particular locations or within particular zones, a requirement that is very difficult to achieve if marking the skin is not possible. We thoroughly searched the literature for experimental evidence and protocol recommendations for safe delivery of Nd:YAP laser stimuli over marked skin, but found nothing. Methods. We designed an experimental protocol to define safe parameters for the use of Nd:YAP laser stimuli over skin that has been marked with black dots, and used thermal imaging to assess the safety of the procedure at the forearm and the back. Results. Using thermal imaging and repeated laser stimulation to ink-marked skin, we demonstrated that skin temperature did not increase progressively across the course of the experiment, and that the small change in temperature seen at the forearm was reversed during the rest periods between blocks. Furthermore, no participant experienced skin damage due to the procedure. Conclusion. This protocol offers parameters for safe, confident and effective experimentation using repeated Nd:YAP laser on skin marked with ink, thus paving the way for investigations that depend on it.
format: application/pdf
format: text/html
creator: Victoria J. Madden
creator: Mark J. Catley
creator: Luzia Grabherr
creator: Francesca Mazzola
creator: Mohammad Shohag
creator: G. Lorimer Moseley
subject: Anesthesiology and Pain Management
subject: Dermatology
subject: Neuroscience
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1577
publisher: PeerJ Inc.
rights: © 2016 Madden et al.
abstract: Background. Nd:YAP laser is widely used to investigate the nociceptive and pain systems, generating perpetual and laser-evoked neurophysiological responses. A major procedural concern for the use of Nd:YAP laser stimuli in experimental research is the risk of skin damage. The absorption of Nd:YAP laser stimuli is greater in darker skin, or in pale skin that has been darkened with ink, prompting some ethics boards to refuse approval to experimenters wishing to track stimulus location by marking the skin with ink. Some research questions, however, require laser stimuli to be delivered at particular locations or within particular zones, a requirement that is very difficult to achieve if marking the skin is not possible. We thoroughly searched the literature for experimental evidence and protocol recommendations for safe delivery of Nd:YAP laser stimuli over marked skin, but found nothing. Methods. We designed an experimental protocol to define safe parameters for the use of Nd:YAP laser stimuli over skin that has been marked with black dots, and used thermal imaging to assess the safety of the procedure at the forearm and the back. Results. Using thermal imaging and repeated laser stimulation to ink-marked skin, we demonstrated that skin temperature did not increase progressively across the course of the experiment, and that the small change in temperature seen at the forearm was reversed during the rest periods between blocks. Furthermore, no participant experienced skin damage due to the procedure. Conclusion. This protocol offers parameters for safe, confident and effective experimentation using repeated Nd:YAP laser on skin marked with ink, thus paving the way for investigations that depend on it.
bibliographic citation: Madden et al. (2016) The effect of repeated laser stimuli to ink-marked skin on skin temperature—recommendations for a safe experimental protocol in humans. PeerJ 4:e1577 https://doi.org/10.7717/peerj.1577
date submitted: 2015-10-02
date accepted: 2015-12-16
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Madden
  given name: Victoria J.
author list: Agent
  family name: Catley
  given name: Mark J.
author list: Agent
  family name: Grabherr
  given name: Luzia
author list: Agent
  family name: Mazzola
  given name: Francesca
author list: Agent
  family name: Shohag
  given name: Mohammad
author list: Agent
  family name: Moseley
  given name: G. Lorimer
doi: 10.7717/peerj.1577
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: ©2016 Madden et al.
attribution name: Madden et al.

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system
type: item
type: AcademicArticle
description: Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.
format: application/pdf
format: text/html
creator: Jordan D. Satler
creator: Amanda J. Zellmer
creator: Bryan C. Carstens
subject: Biodiversity
subject: Biogeography
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.1576
publisher: PeerJ Inc.
rights: © 2016 Satler et al.
abstract: Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.
bibliographic citation: Satler et al. (2016) Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system. PeerJ 4:e1576 https://doi.org/10.7717/peerj.1576
date submitted: 2015-09-03
date accepted: 2015-12-16
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Satler
  given name: Jordan D.
author list: Agent
  family name: Zellmer
  given name: Amanda J.
author list: Agent
  family name: Carstens
  given name: Bryan C.
doi: 10.7717/peerj.1576
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: ©2016 Satler et al.
attribution name: Satler et al.

Faces in commonly experienced configurations enter awareness faster due to their curvature relative to fixation
type: item
type: AcademicArticle
description: The extent to which perceptually suppressed face stimuli are still processed has been extensively studied using the continuous flash suppression paradigm (CFS). Studies that rely on breaking CFS (b-CFS), in which the time it takes for an initially suppressed stimulus to become detectable is measured, have provided evidence for relatively complex processing of invisible face stimuli. In contrast, adaptation and neuroimaging studies have shown that perceptually suppressed faces are only processed for a limited set of features, such as its general shape. In this study, we asked whether perceptually suppressed face stimuli presented in their commonly experienced configuration would break suppression faster than when presented in an uncommonly experienced configuration. This study was motivated by a recent neuroimaging study showing that commonly experienced face configurations are more strongly represented in the fusiform face area. Our findings revealed that faces presented in commonly experienced configurations indeed broke suppression faster, yet this effect did not interact with face inversion suggesting that, in a b-CFS context, perceptually suppressed faces are potentially not processed by specialized (high-level) face processing mechanisms. Rather, our pattern of results is consistent with an interpretation based on the processing of more basic visual properties such as convexity.
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creator: Pieter Moors
creator: Johan Wagemans
creator: Lee de-Wit
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1565
publisher: PeerJ Inc.
rights: © 2016 Moors et al.
abstract: The extent to which perceptually suppressed face stimuli are still processed has been extensively studied using the continuous flash suppression paradigm (CFS). Studies that rely on breaking CFS (b-CFS), in which the time it takes for an initially suppressed stimulus to become detectable is measured, have provided evidence for relatively complex processing of invisible face stimuli. In contrast, adaptation and neuroimaging studies have shown that perceptually suppressed faces are only processed for a limited set of features, such as its general shape. In this study, we asked whether perceptually suppressed face stimuli presented in their commonly experienced configuration would break suppression faster than when presented in an uncommonly experienced configuration. This study was motivated by a recent neuroimaging study showing that commonly experienced face configurations are more strongly represented in the fusiform face area. Our findings revealed that faces presented in commonly experienced configurations indeed broke suppression faster, yet this effect did not interact with face inversion suggesting that, in a b-CFS context, perceptually suppressed faces are potentially not processed by specialized (high-level) face processing mechanisms. Rather, our pattern of results is consistent with an interpretation based on the processing of more basic visual properties such as convexity.
bibliographic citation: Moors et al. (2016) Faces in commonly experienced configurations enter awareness faster due to their curvature relative to fixation. PeerJ 4:e1565 https://doi.org/10.7717/peerj.1565
date submitted: 2015-10-12
date accepted: 2015-12-14
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moors
  given name: Pieter
author list: Agent
  family name: Wagemans
  given name: Johan
author list: Agent
  family name: de-Wit
  given name: Lee
doi: 10.7717/peerj.1565
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: © 2016 Moors et al.
attribution name: Moors et al.

A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors
type: item
type: AcademicArticle
description: Background. Mobile health and digital medicine technologies are becoming increasingly used by individuals with common, chronic diseases to monitor their health. Numerous devices, sensors, and apps are available to patients and consumers–some of which have been shown to lead to improved health management and health outcomes. However, no randomized controlled trials have been conducted which examine health care costs, and most have failed to provide study participants with a truly comprehensive monitoring system. Methods. We conducted a prospective randomized controlled trial of adults who had submitted a 2012 health insurance claim associated with hypertension, diabetes, and/or cardiac arrhythmia. The intervention involved receipt of one or more mobile devices that corresponded to their condition(s) (hypertension: Withings Blood Pressure Monitor; diabetes: Sanofi iBGStar Blood Glucose Meter; arrhythmia: AliveCor Mobile ECG) and an iPhone with linked tracking applications for a period of 6 months; the control group received a standard disease management program. Moreover, intervention study participants received access to an online health management system which provided participants detailed device tracking information over the course of the study. This was a monitoring system designed by leveraging collaborations with device manufacturers, a connected health leader, health care provider, and employee wellness program–making it both unique and inclusive. We hypothesized that health resource utilization with respect to health insurance claims may be influenced by the monitoring intervention. We also examined health-self management. Results & Conclusions. There was little evidence of differences in health care costs or utilization as a result of the intervention. Furthermore, we found evidence that the control and intervention groups were equivalent with respect to most health care utilization outcomes. This result suggests there are not large short-term increases or d…
format: application/pdf
format: text/html
creator: Cinnamon S. Bloss
creator: Nathan E. Wineinger
creator: Melissa Peters
creator: Debra L. Boeldt
creator: Lauren Ariniello
creator: Ju Young Kim
creator: Judith Sheard
creator: Ravi Komatireddy
creator: Paddy Barrett
creator: Eric J. Topol
subject: Clinical Trials
subject: Health Policy
subject: Translational Medicine
description: doi:10.7717/peerj.1554
publisher: PeerJ Inc.
rights: © 2016 Bloss et al.
abstract: Background. Mobile health and digital medicine technologies are becoming increasingly used by individuals with common, chronic diseases to monitor their health. Numerous devices, sensors, and apps are available to patients and consumers–some of which have been shown to lead to improved health management and health outcomes. However, no randomized controlled trials have been conducted which examine health care costs, and most have failed to provide study participants with a truly comprehensive monitoring system. Methods. We conducted a prospective randomized controlled trial of adults who had submitted a 2012 health insurance claim associated with hypertension, diabetes, and/or cardiac arrhythmia. The intervention involved receipt of one or more mobile devices that corresponded to their condition(s) (hypertension: Withings Blood Pressure Monitor; diabetes: Sanofi iBGStar Blood Glucose Meter; arrhythmia: AliveCor Mobile ECG) and an iPhone with linked tracking applications for a period of 6 months; the control group received a standard disease management program. Moreover, intervention study participants received access to an online health management system which provided participants detailed device tracking information over the course of the study. This was a monitoring system designed by leveraging collaborations with device manufacturers, a connected health leader, health care provider, and employee wellness program–making it both unique and inclusive. We hypothesized that health resource utilization with respect to health insurance claims may be influenced by the monitoring intervention. We also examined health-self management. Results & Conclusions. There was little evidence of differences in health care costs or utilization as a result of the intervention. Furthermore, we found evidence that the control and intervention groups were equivalent with respect to most health care utilization outcomes. This result suggests there are not large short-term increases or d…
bibliographic citation: Bloss et al. (2016) A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors. PeerJ 4:e1554 https://doi.org/10.7717/peerj.1554
date submitted: 2016-01-1
date accepted: 2015-12-11
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bloss
  given name: Cinnamon S.
author list: Agent
  family name: Wineinger
  given name: Nathan E.
author list: Agent
  family name: Peters
  given name: Melissa
author list: Agent
  family name: Boeldt
  given name: Debra L.
author list: Agent
  family name: Ariniello
  given name: Lauren
author list: Agent
  family name: Kim
  given name: Ju Young
author list: Agent
  family name: Sheard
  given name: Judith
author list: Agent
  family name: Komatireddy
  given name: Ravi
author list: Agent
  family name: Barrett
  given name: Paddy
author list: Agent
  family name: Topol
  given name: Eric J.
doi: 10.7717/peerj.1554
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: © 2016 Bloss et al.
attribution name: Bloss et al.

Residual mitochondrial transmembrane potential decreases unsaturated fatty acid level in sake yeast during alcoholic fermentation
type: item
type: AcademicArticle
description: Oxygen, a key nutrient in alcoholic fermentation, is rapidly depleted during this process. Several pathways of oxygen utilization have been reported in the yeast Saccharomyces cerevisiae during alcoholic fermentation, namely synthesis of unsaturated fatty acid, sterols and heme, and the mitochondrial electron transport chain. However, the interaction between these pathways has not been investigated. In this study, we showed that the major proportion of unsaturated fatty acids of ester-linked lipids in sake fermentation mash is derived from the sake yeast rather than from rice or koji (rice fermented with Aspergillus). Additionally, during alcoholic fermentation, inhibition of the residual mitochondrial activity of sake yeast increases the levels of unsaturated fatty acids of ester-linked lipids. These findings indicate that the residual activity of the mitochondrial electron transport chain reduces molecular oxygen levels and decreases the synthesis of unsaturated fatty acids, thereby increasing the synthesis of estery flavors by sake yeast. This is the first report of a novel link between residual mitochondrial transmembrane potential and the synthesis of unsaturated fatty acids by the brewery yeast during alcoholic fermentation.
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format: text/html
creator: Kazutaka Sawada
creator: Hiroshi Kitagaki
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.1552
publisher: PeerJ Inc.
rights: © 2016 Sawada & Kitagaki
abstract: Oxygen, a key nutrient in alcoholic fermentation, is rapidly depleted during this process. Several pathways of oxygen utilization have been reported in the yeast Saccharomyces cerevisiae during alcoholic fermentation, namely synthesis of unsaturated fatty acid, sterols and heme, and the mitochondrial electron transport chain. However, the interaction between these pathways has not been investigated. In this study, we showed that the major proportion of unsaturated fatty acids of ester-linked lipids in sake fermentation mash is derived from the sake yeast rather than from rice or koji (rice fermented with Aspergillus). Additionally, during alcoholic fermentation, inhibition of the residual mitochondrial activity of sake yeast increases the levels of unsaturated fatty acids of ester-linked lipids. These findings indicate that the residual activity of the mitochondrial electron transport chain reduces molecular oxygen levels and decreases the synthesis of unsaturated fatty acids, thereby increasing the synthesis of estery flavors by sake yeast. This is the first report of a novel link between residual mitochondrial transmembrane potential and the synthesis of unsaturated fatty acids by the brewery yeast during alcoholic fermentation.
bibliographic citation: Sawada et al. (2016) Residual mitochondrial transmembrane potential decreases unsaturated fatty acid level in sake yeast during alcoholic fermentation. PeerJ 4:e1552 https://doi.org/10.7717/peerj.1552
date submitted: 2015-09-22
date accepted: 2015-12-10
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sawada
  given name: Kazutaka
author list: Agent
  family name: Kitagaki
  given name: Hiroshi
doi: 10.7717/peerj.1552
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: © 2016 Sawada & Kitagaki
attribution name: Sawada & Kitagaki

The impact of land reform on the status of large carnivores in Zimbabwe
type: item
type: AcademicArticle
description: Large carnivores are decreasing in number due to growing pressure from an expanding human population. It is increasingly recognised that state-protected conservation areas are unlikely to be sufficient to protect viable populations of large carnivores, and that private land will be central to conservation efforts. In 2000, a fast-track land reform programme (FTLRP) was initiated in Zimbabwe, ostensibly to redress the racial imbalance in land ownership, but which also had the potential to break up large areas of carnivore habitat on private land. To date, research has focused on the impact of the FTLRP process on the different human communities, while impacts on wildlife have been overlooked. Here we provide the first systematic assessment of the impact of the FTLRP on the status of large carnivores. Spoor counts were conducted across private, resettled and communal land use types in order to estimate the abundance of large carnivores, and to determine how this had been affected by land reform. The density of carnivore spoor differed significantly between land use types, and was lower on resettlement land than on private land, suggesting that the resettlement process has resulted in a substantial decline in carnivore abundance. Habitat loss and high levels of poaching in and around resettlement areas are the most likely causes. The FTLRP resulted in the large-scale conversion of land that was used sustainably and productively for wildlife into unsustainable, unproductive agricultural land uses. We recommended that models of land reform should consider the type of land available, that existing expertise in land management should be retained where possible, and that resettlement programmes should be carefully planned in order to minimise the impacts on wildlife and on people.
format: application/pdf
format: text/html
creator: Samual T. Williams
creator: Kathryn S. Williams
creator: Christoffel J. Joubert
creator: Russell A. Hill
subject: Biodiversity
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.1537
publisher: PeerJ Inc.
rights: © 2016 Williams et al.
abstract: Large carnivores are decreasing in number due to growing pressure from an expanding human population. It is increasingly recognised that state-protected conservation areas are unlikely to be sufficient to protect viable populations of large carnivores, and that private land will be central to conservation efforts. In 2000, a fast-track land reform programme (FTLRP) was initiated in Zimbabwe, ostensibly to redress the racial imbalance in land ownership, but which also had the potential to break up large areas of carnivore habitat on private land. To date, research has focused on the impact of the FTLRP process on the different human communities, while impacts on wildlife have been overlooked. Here we provide the first systematic assessment of the impact of the FTLRP on the status of large carnivores. Spoor counts were conducted across private, resettled and communal land use types in order to estimate the abundance of large carnivores, and to determine how this had been affected by land reform. The density of carnivore spoor differed significantly between land use types, and was lower on resettlement land than on private land, suggesting that the resettlement process has resulted in a substantial decline in carnivore abundance. Habitat loss and high levels of poaching in and around resettlement areas are the most likely causes. The FTLRP resulted in the large-scale conversion of land that was used sustainably and productively for wildlife into unsustainable, unproductive agricultural land uses. We recommended that models of land reform should consider the type of land available, that existing expertise in land management should be retained where possible, and that resettlement programmes should be carefully planned in order to minimise the impacts on wildlife and on people.
bibliographic citation: Williams et al. (2016) The impact of land reform on the status of large carnivores in Zimbabwe. PeerJ 4:e1537 https://doi.org/10.7717/peerj.1537
date submitted: 2015-07-25
date accepted: 2015-12-06
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williams
  given name: Samual T.
author list: Agent
  family name: Williams
  given name: Kathryn S.
author list: Agent
  family name: Joubert
  given name: Christoffel J.
author list: Agent
  family name: Hill
  given name: Russell A.
doi: 10.7717/peerj.1537
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: © 2016 Williams et al.
attribution name: Williams et al.

Probable impact of age and hypoxia on proliferation and microRNA expression profile of bone marrow-derived human mesenchymal stem cells
type: item
type: AcademicArticle
description: Decline in the therapeutic potential of bone marrow-derived mesenchymal stem cells (MSC) is often seen with older donors as compared to young. Although hypoxia is known as an approach to improve the therapeutic potential of MSC in term of cell proliferation and differentiation capacity, its effects on MSC from aged donors have not been well studied. To evaluate the influence of hypoxia on different age groups, MSC from young (<30 years) and aged (>60 years) donors were expanded under hypoxic (5% O2) and normal (20% O2) culture conditions. MSC from old donors exhibited a reduction in proliferation rate and differentiation potential together with the accumulation of senescence features compared to that of young donors. However, MSC cultured under hypoxic condition showed enhanced self-renewing and proliferation capacity in both age groups as compared to normal condition. Bioinformatic analysis of the gene ontology (GO) and KEGG pathway under hypoxic culture condition identified hypoxia-inducible miRNAs that were found to target transcriptional activity leading to enhanced cell proliferation, migration as well as decrease in growth arrest and apoptosis through the activation of multiple signaling pathways. Overall, differentially expressed miRNA provided additional information to describe the biological changes of young and aged MSCs expansion under hypoxic culture condition at the molecular level. Based on our findings, the therapeutic potential hierarchy of MSC according to donor’s age group and culture conditions can be categorized in the following order: young (hypoxia) > young (normoxia) > old aged (hypoxia) > old aged (normoxia).
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format: text/html
creator: Norlaily Mohd Ali
creator: Lily Boo
creator: Swee Keong Yeap
creator: Huynh Ky
creator: Dilan A. Satharasinghe
creator: Woan Charn Liew
creator: Han Kiat Ong
creator: Soon Keng Cheong
creator: Tunku Kamarul
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.1536
publisher: PeerJ Inc.
rights: © 2016 Mohd Ali et al.
abstract: Decline in the therapeutic potential of bone marrow-derived mesenchymal stem cells (MSC) is often seen with older donors as compared to young. Although hypoxia is known as an approach to improve the therapeutic potential of MSC in term of cell proliferation and differentiation capacity, its effects on MSC from aged donors have not been well studied. To evaluate the influence of hypoxia on different age groups, MSC from young (<30 years) and aged (>60 years) donors were expanded under hypoxic (5% O2) and normal (20% O2) culture conditions. MSC from old donors exhibited a reduction in proliferation rate and differentiation potential together with the accumulation of senescence features compared to that of young donors. However, MSC cultured under hypoxic condition showed enhanced self-renewing and proliferation capacity in both age groups as compared to normal condition. Bioinformatic analysis of the gene ontology (GO) and KEGG pathway under hypoxic culture condition identified hypoxia-inducible miRNAs that were found to target transcriptional activity leading to enhanced cell proliferation, migration as well as decrease in growth arrest and apoptosis through the activation of multiple signaling pathways. Overall, differentially expressed miRNA provided additional information to describe the biological changes of young and aged MSCs expansion under hypoxic culture condition at the molecular level. Based on our findings, the therapeutic potential hierarchy of MSC according to donor’s age group and culture conditions can be categorized in the following order: young (hypoxia) > young (normoxia) > old aged (hypoxia) > old aged (normoxia).
bibliographic citation: Mohd Ali et al. (2016) Probable impact of age and hypoxia on proliferation and microRNA expression profile of bone marrow-derived human mesenchymal stem cells. PeerJ 4:e1536 https://doi.org/10.7717/peerj.1536
date submitted: 2015-09-01
date accepted: 2015-12-05
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohd Ali
  given name: Norlaily
author list: Agent
  family name: Boo
  given name: Lily
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Ky
  given name: Huynh
author list: Agent
  family name: Satharasinghe
  given name: Dilan A.
author list: Agent
  family name: Liew
  given name: Woan Charn
author list: Agent
  family name: Ong
  given name: Han Kiat
author list: Agent
  family name: Cheong
  given name: Soon Keng
author list: Agent
  family name: Kamarul
  given name: Tunku
doi: 10.7717/peerj.1536
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: © 2016 Mohd Ali et al.
attribution name: Mohd Ali et al.

Preoperative CT versus diffusion weighted magnetic resonance imaging of the liver in patients with rectal cancer; a prospective randomized trial
type: item
type: AcademicArticle
description: Introduction. Colorectal cancer is one of the most frequent cancers in the world and liver metastases are seen in up to 19% of patients with colorectal cancers. Detection of liver metastases is not only vital for sufficient treatment and survival, but also for a better estimation of prognosis. The aim of this study was to evaluate the feasibility of diffusion weighted MRI of the liver as part of a combined MR evaluation of patients with rectal cancers and compare it with the standard preoperative evaluation of the liver with CT. Methods. Consecutive patients diagnosed with rectal cancers were asked to participate in the study. Preoperative CT and diffusion weighted MR (DWMR) were compared to contrast enhanced laparoscopic ultrasound (CELUS). Results. A total of 35 patients were included, 15 patients in Group-1 having the standard CT evaluation of the liver and 20 patients in Group-2 having the standard CT evaluation of the liver and DWMR of the liver. Compared with CELUS, the per-patient sensitivity/specificity was 50/100% for CT, and for DWMR: 100/94% and 100/100% for Reader 1 and 2, respectively. The per-lesion sensitivity of CT and DWMR were 17% and 89%, respectively compared with CELUS. Furthermore, one patient had non-resectable metastases after DWMR despite being diagnosed with resectable metastases after CT. Another patient was diagnosed with multiple liver metastases during CELUS, despite a negative CT-scan. Discussion. DWMR is feasible for preoperative evaluation of liver metastases. The current standard preoperative evaluation with CT-scan results in disadvantages like missed metastases and futile operations. We recommend that patients with rectal cancer, who are scheduled for MR of the rectum, should have a DWMR of the liver performed at the same time.
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creator: Michael P. Achiam
creator: Vibeke B. Løgager
creator: Bjørn Skjoldbye
creator: Jakob M. Møller
creator: Torben Lorenzen
creator: Vera L. Rasmussen
creator: Henrik S. Thomsen
creator: Talie H. Mollerup
creator: Cecilie Okholm
creator: Jacob Rosenberg
subject: Clinical Trials
subject: Gastroenterology and Hepatology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1532
publisher: PeerJ Inc.
rights: © 2016 Achiam et al.
abstract: Introduction. Colorectal cancer is one of the most frequent cancers in the world and liver metastases are seen in up to 19% of patients with colorectal cancers. Detection of liver metastases is not only vital for sufficient treatment and survival, but also for a better estimation of prognosis. The aim of this study was to evaluate the feasibility of diffusion weighted MRI of the liver as part of a combined MR evaluation of patients with rectal cancers and compare it with the standard preoperative evaluation of the liver with CT. Methods. Consecutive patients diagnosed with rectal cancers were asked to participate in the study. Preoperative CT and diffusion weighted MR (DWMR) were compared to contrast enhanced laparoscopic ultrasound (CELUS). Results. A total of 35 patients were included, 15 patients in Group-1 having the standard CT evaluation of the liver and 20 patients in Group-2 having the standard CT evaluation of the liver and DWMR of the liver. Compared with CELUS, the per-patient sensitivity/specificity was 50/100% for CT, and for DWMR: 100/94% and 100/100% for Reader 1 and 2, respectively. The per-lesion sensitivity of CT and DWMR were 17% and 89%, respectively compared with CELUS. Furthermore, one patient had non-resectable metastases after DWMR despite being diagnosed with resectable metastases after CT. Another patient was diagnosed with multiple liver metastases during CELUS, despite a negative CT-scan. Discussion. DWMR is feasible for preoperative evaluation of liver metastases. The current standard preoperative evaluation with CT-scan results in disadvantages like missed metastases and futile operations. We recommend that patients with rectal cancer, who are scheduled for MR of the rectum, should have a DWMR of the liver performed at the same time.
bibliographic citation: Achiam et al. (2016) Preoperative CT versus diffusion weighted magnetic resonance imaging of the liver in patients with rectal cancer; a prospective randomized trial. PeerJ 4:e1532 https://doi.org/10.7717/peerj.1532
date submitted: 2015-09-01
date accepted: 2015-12-03
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Achiam
  given name: Michael P.
author list: Agent
  family name: Løgager
  given name: Vibeke B.
author list: Agent
  family name: Skjoldbye
  given name: Bjørn
author list: Agent
  family name: Møller
  given name: Jakob M.
author list: Agent
  family name: Lorenzen
  given name: Torben
author list: Agent
  family name: Rasmussen
  given name: Vera L.
author list: Agent
  family name: Thomsen
  given name: Henrik S.
author list: Agent
  family name: Mollerup
  given name: Talie H.
author list: Agent
  family name: Okholm
  given name: Cecilie
author list: Agent
  family name: Rosenberg
  given name: Jacob
doi: 10.7717/peerj.1532
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: ©2016 Achiam et al.
attribution name: Achiam et al.

Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus
type: item
type: AcademicArticle
description: Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.
format: application/pdf
format: text/html
creator: Felipe Coutinho
creator: Diogo Antonio Tschoeke
creator: Fabiano Thompson
creator: Cristiane Thompson
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.1522
publisher: PeerJ Inc.
rights: © 2016 Coutinho et al.
abstract: Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.
bibliographic citation: Coutinho et al. (2016) Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus. PeerJ 4:e1522 https://doi.org/10.7717/peerj.1522
date submitted: 2015-05-26
date accepted: 2015-11-28
issued: 2016-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coutinho
  given name: Felipe
author list: Agent
  family name: Tschoeke
  given name: Diogo Antonio
author list: Agent
  family name: Thompson
  given name: Fabiano
author list: Agent
  family name: Thompson
  given name: Cristiane
doi: 10.7717/peerj.1522
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-14
copyright: © 2016 Coutinho et al.
attribution name: Coutinho et al.

Acute hypothalamic suppression significantly affects trabecular bone but not cortical bone following recovery and ovariectomy surgery in a rat model
type: item
type: AcademicArticle
description: Background. Osteoporosis is “a pediatric disease with geriatric consequences.” Bone morphology and tissue quality co-adapt during ontogeny for sufficient bone stiffness. Altered bone morphology from hypothalamic amenorrhea, a risk factor for low bone mass in women, may affect bone strength later in life. Our purpose was to determine if altered morphology following hypothalamic suppression during development affects cortical bone strength and trabecular bone volume (BV/TV) at maturity. Methods. Female rats (25 days old) were assigned to a control (C) group (n = 45) that received saline injections (.2 cc) or an experimental group (GnRH-a) (n = 45) that received gonadotropin releasing hormone antagonist injections (.24 mg per dose) for 25 days. Fifteen animals from each group were sacrificed immediately after the injection protocol at Day 50 (C, GnRH-a). The remaining animals recovered for 135 days and a subset of each group was sacrificed at Day 185 ((C-R) (n = 15) and (G-R) (n = 15)). The remaining animals had an ovariectomy surgery (OVX) at 185 days of age and were sacrificed 40 days later (C-OVX) (n = 15) and (G-OVX) (n = 15). After sacrifice femurs were mechanically tested and scanned using micro CT. Serum C-terminal telopeptides (CTX) and insulin-like growth factor 1 (IGF-1) were measured. Two-way ANOVA (2 groups (GnRH-a and Control) X 3 time points (Injection Protocol, Recovery, post-OVX)) was computed. Results. GnRH-a injections suppressed uterine weights (72%) and increased CTX levels by 59%. Bone stiffness was greater in the GnRH-a groups compared to C. Ash content and cortical bone area were similar between groups at all time points. Polar moment of inertia, a measure of bone architecture, was 15% larger in the GnRH-a group and remained larger than C (19%) following recovery. Both the polar moment of inertia and cortical area increased linearly with the increases in body weight. Following the injection protocol, trabecular BV/TV was 31% lower in the GnRH-a g…
format: application/pdf
format: text/html
creator: Vanessa R. Yingling
creator: Kathryn A. Mitchell
creator: Megan Lunny
subject: Anatomy and Physiology
subject: Diabetes and Endocrinology
subject: Kinesiology
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1575
publisher: PeerJ Inc.
rights: © 2016 Yingling et al.
abstract: Background. Osteoporosis is “a pediatric disease with geriatric consequences.” Bone morphology and tissue quality co-adapt during ontogeny for sufficient bone stiffness. Altered bone morphology from hypothalamic amenorrhea, a risk factor for low bone mass in women, may affect bone strength later in life. Our purpose was to determine if altered morphology following hypothalamic suppression during development affects cortical bone strength and trabecular bone volume (BV/TV) at maturity. Methods. Female rats (25 days old) were assigned to a control (C) group (n = 45) that received saline injections (.2 cc) or an experimental group (GnRH-a) (n = 45) that received gonadotropin releasing hormone antagonist injections (.24 mg per dose) for 25 days. Fifteen animals from each group were sacrificed immediately after the injection protocol at Day 50 (C, GnRH-a). The remaining animals recovered for 135 days and a subset of each group was sacrificed at Day 185 ((C-R) (n = 15) and (G-R) (n = 15)). The remaining animals had an ovariectomy surgery (OVX) at 185 days of age and were sacrificed 40 days later (C-OVX) (n = 15) and (G-OVX) (n = 15). After sacrifice femurs were mechanically tested and scanned using micro CT. Serum C-terminal telopeptides (CTX) and insulin-like growth factor 1 (IGF-1) were measured. Two-way ANOVA (2 groups (GnRH-a and Control) X 3 time points (Injection Protocol, Recovery, post-OVX)) was computed. Results. GnRH-a injections suppressed uterine weights (72%) and increased CTX levels by 59%. Bone stiffness was greater in the GnRH-a groups compared to C. Ash content and cortical bone area were similar between groups at all time points. Polar moment of inertia, a measure of bone architecture, was 15% larger in the GnRH-a group and remained larger than C (19%) following recovery. Both the polar moment of inertia and cortical area increased linearly with the increases in body weight. Following the injection protocol, trabecular BV/TV was 31% lower in the GnRH-a g…
bibliographic citation: Yingling et al. (2016) Acute hypothalamic suppression significantly affects trabecular bone but not cortical bone following recovery and ovariectomy surgery in a rat model. PeerJ 4:e1575 https://doi.org/10.7717/peerj.1575
date submitted: 2015-09-11
date accepted: 2015-12-16
issued: 2016-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yingling
  given name: Vanessa R.
author list: Agent
  family name: Mitchell
  given name: Kathryn A.
author list: Agent
  family name: Lunny
  given name: Megan
doi: 10.7717/peerj.1575
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-12
copyright: ©2016 Yingling et al.
attribution name: Yingling et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359